Changes in motion velocities (i.e. accelerations in all 3-D directions) apply inertia forces on the ship.
'Motion veocities' and 'inertia forces'? You don't even sound like an engineer.
Yes, there are forces applied on the ship in all three dimensions, but the design of the ship's propulsion systems, and its navigational systems, consider the motion in two dimensions. It has no need to correct for up and down forces produced by waves because they are self-cancelling. After it has ridden up a large wave or swell it must go down again, and it will always, no matter what sea conditions are, arrive at its destination on the same level as the port. It only has to correct for lateral deflections in order to arrive at its destination, and any retardation or acceleration of its forward motion will simply make it early or late.
Space travel not only has forces acting in all three dimensions but they do not cancel out and the navigation of the vessel must consider its motion in all three dimensions or else it will miss its target entirely. Any deviation in any direction must be corrected or it will not arrive where it intends to be at all.
So the forces applied to a seafaring vessel may be more complex than those on a spacecraft, but the
navigation concerns of any vessel travelling over the surface of the Earth are considerably simpler.